I think I had this problem with one of the early versions of the 1.1 patch, and I want to say that by finishing the deal between Vault 15 and NCR made my car re-appear on the shiny new Vault 15 city map. Might be worth a shot, unless you're going for some kind of NCR opposed run.
I've found a strange explosion script bug that I think is only in your patch, as the first time it happened, I was able to re-install the unpatched version, and move on.
So, as far as I can tell, this bug triggers when you save in a room in which an object has an explosion script, and then...
With the most recent version of the patch(The Feb 6 one) I had a save at the bridgekeeper encounter, that I reverted to to try to use the new version of the nearby village quest since my old one was bugged.
However, either having the bridgekeeper instakill me, or me instakilling him via the...